Shotgun Metagenomic Sequencing Analysis of Soft-Rot Enterobacteriaceae in Polymicrobial Communities

  • James Doonan
  • Sandra Denman
  • James E. McDonald
  • Peter N. GolyshinEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1539)


Shotgun metagenomic sequencing of bacterial communities in necrotic plant lesions allows insights of host–pathogen molecular interactions. Soft-rot Enterobacteriaceae are significant crop pathogens with a wide host range. Reconstructed polymicrobial community DNA from soft-rot affected crops provides details of species relative abundance and functional potential, enabling significant insights into their lifestyle. Here, we describe a workflow for DNA recovery, metagenomic shotgun sequencing and in particular, an in silico analysis of bacterial isolates from affected plant tissue.

Key words

Shotgun metagenomics Host–pathogen molecular interactions Soft-rot Enterobacteriaceae Polymicrobial In silico 


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • James Doonan
    • 1
  • Sandra Denman
    • 2
  • James E. McDonald
    • 1
  • Peter N. Golyshin
    • 1
    Email author
  1. 1.School of Biological SciencesBangor UniversityBangorUK
  2. 2.Centre for Ecosystems Society and BiosecurityForest ResearchSurreyUK

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